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- even if intend to write to a "new" file, if file exists and a symlink, it would write into a file pointed by the symlink... (well -- to say the truth -- this behavior is consistent with e.g. how
>in shell works):
In [1]: import nibabel as nibIn [2]:!ln -s nonexistent out.nii.gzIn [3]:!ls -l nonexistent out.nii.gzls: cannot access'nonexistent': No such file or directorylrwxrwxrwx 1 yoh yoh 11 Jul 28 23:29 out.nii.gz -> nonexistent*In [7]: nib.Nifti1Image(np.arange(12).reshape((2,2,3)), None, None).to_filename('out.nii.gz')In [8]:!ls -l nonexistent out.nii.gz-rw------- 1 yoh yoh 96 Jul 28 23:30 nonexistentlrwxrwxrwx 1 yoh yoh 11 Jul 28 23:29 out.nii.gz -> nonexistent
- if file pointed by a symlink exists but with permissions removed for writing (belongs to other user, or explicitly write bit removed, e.g. under annex):
In [9]: !chmod a-w nonexistentIn [10]: nib.Nifti1Image(np.arange(12).reshape((2,2,3)), None, None).to_filename('out.nii.gz').../home/yoh/proj/nipy/nipy-suite/nibabel/nibabel/openers.py in _gzip_open(fileish, *args, **kwargs) 62 63 def _gzip_open(fileish, *args, **kwargs):---> 64 gzip_file = BufferedGzipFile(fileish, *args, **kwargs) 65 66 # Speedup for #209; attribute not present in in Python 3.5/usr/lib/python2.7/gzip.pyc in __init__(self, filename, mode, compresslevel, fileobj, mtime) 92 mode += 'b' 93 if fileobj is None:---> 94 fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb') 95 if filename is None: 96 # Issue #13781: os.fdopen() creates a fileobj with a bogus nameIOError: [Errno 13] Permission denied: 'out.nii.gz'I wondered... would it be sensible to suggest to first remove the file intended to be written to (at least in to_filename) before writing? that would allow to interact with git-annex'ed datasets more easily,
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